MolNFT v1 · #99157 · protein
Crystal structure of inositol 1,3,4,5,6-pentakisphosphate 2-kinase E82C/S142C
4LV7 · Inositol-pentakisphosphate 2-kinase: “Crystal structure of inositol 1,3,4,5,6-pentakisphosphate 2-kinase E82C/S142C”. X-ray diffraction, 4 ligands (IHP, ADP, MG), 4 pockets (best druggability 0.84). MolNFT v1 #99157 on GenesisL1: 3D…
- PDB
- 4LV7
- Type
- protein
- Length
- 784 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Inositol-pentakisphosphate 2-kinase
- EC
- 2.7.1.158
- UniProt
- Q93YN9
- Ligands
- IHP, ADP, MG, ZN
- Pockets
- 4 · best druggability 0.84
Structure
x-ray diffraction · 2 distinct chains · 44% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Inositol-pentakisphosphate 2-kinase (EC 2.7.1.158) | protein | 390 | 45% helix, 17% strand | Q93YN9 |
| B | Inositol-pentakisphosphate 2-kinase (EC 2.7.1.158) | protein | 394 | 43% helix, 17% strand | Q93YN9 |
Ligands and binding sites
- IHP · Inositol hexakisphosphate · ligand · 2 copies · chains A, B
- ADP · Adenosine-5'-diphosphate · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
- ZN · Zinc ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 996 | 0.84 | 0.84 | 91 | IHP, ADP, MG |
| 2 | 1184 | 0.82 | 0.83 | 120 | IHP, ADP, MG |
| 3 | 419 | 0.64 | 0.78 | 42 | empty |
| 4 | 195 | 0.46 | 0.74 | 33 | empty |
Interfaces
1 interface between chains.
- A–B · 656 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 4LV7 · Crystal structure of inositol 1,3,4,5,6-pentakisphosphate 2-kinase E82C/S142C · the same entry in another collection · chain A against A, TM-score 1.00
- Q93YN9 · AlphaFold monomer V2.0 prediction for inositol-pentakisphosphate 2-kinase (Q93YN9) · a predicted model of the same protein · chain B against A, TM-score 0.99
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt Q93YN9
- Elsewhere: RCSB PDB 4LV7 · PDBe 4LV7 · UniProt Q93YN9
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